"Are the auto manufacturers, AAA, small engine makers and U.S. Coast Guard wrong and how can the EPA continue to ignore these concerns," he added.

McCarthy reiterated her confidence in the E15 fuel blend and said lengthy testing has been done.

"What I can tell you is EPA with the [Energy Department] did extensive testing of E15 on cars," McCarthy said.

"We understand that there are challenges prior to 2001, which is when more robust engines were required. We continue to believe E15 is appropriate and, where available, is being used by vehicles that are 2001 and younger."

Many biofuel companies cried foul after seeing a leaked copy of the EPA draft, which they say favors the oil and gas industry.

In the past month, biofuel companies and members of the oil industry have met with the Office of Management and Budget. The White House has hosted nearly 20 meetings on the renewable fuel standard.

"The rule to set limits for 2014 is soon to be proposed," McCarthy said on Thursday. "But will take some time [to finalize]."